Racial/Ethnic Disparities in Genomic Sequencing

Abstract

Importance: Although poorly understood, there is heterogeneity in the molecular biology of cancer across race and ethnicities. The representation of racial minorities in large genomic sequencing efforts is unclear, and could have an impact on health care disparities.

Objective: To determine the racial distribution among samples sequenced within The Cancer Genome Atlas (TCGA) and the deficit of samples needed to detect moderately common mutational frequencies in racial minorities.

Design, setting, and participants: This was a retrospective review of individual patient data from TCGA data portal accessed in July 2015. TCGA comprises samples from a wide array of institutions primarily across the United States. Samples from 10 of the 31 currently available tumor types were analyzed, comprising 5729 samples from the approximately 11 000 available.

Main outcomes and measures: Using the estimated median somatic mutational frequency, the samples needed beyond TCGA to detect a 10% and 5% mutational frequency over the background somatic mutation frequency were calculated for each tumor type by racial ethnicity.

Results: Of the 5729 samples, 77% (n = 4389) were white, 12% (n = 660) were black, 3% (n = 173) were Asian, 3% (n = 149) were Hispanic, and less than 0.5% combined were from patients of Native Hawaiian, Pacific Islander, Alaskan Native, or American Indian decent. This overrepresents white patients compared with the US population and underrepresents primarily Asian and Hispanic patients. With a somatic mutational frequency of 0.7 (prostate cancer) to 9.9 (lung squamous cell cancer), all tumor types from white patients contained enough samples to detect a 10% mutational frequency. This is in contrast to all other racial ethnicities, for which group-specific mutations with 10% frequency would be detectable only for black patients with breast cancer. Group-specific mutations with 5% frequency would be undetectable in any racial minority, but detectable in white patients for all cancer types except lung (adenocarcinoma and squamous cell carcinoma) and colon cancer.

Conclusions and relevance: It is probable, but poorly understood, that ethnic diversity is related to the pathogenesis of cancer, and may have an impact on the generalizability of findings from TCGA to racial minorities. Despite the important benefits that continue to be gained from genomic sequencing, dedicated efforts are needed to avoid widening the already pervasive gap in health care disparities.

Conflict of interest statement

Disclosures: Dr Feng serves on the advisory boards of Medivation/Astellas, GenomeDx, Nanostring, and Celgene. No other disclosures are reported.

Figures

Figure. Numbers of Samples by Race/Ethnicity Needed to Detect 10% and 5% Mutational Frequencies Above 10 Cancers' Background Mutational Frequency Rate Sequenced by TCGA

A, Numbers to detect a 10% mutational frequency. B, Numbers to detect a 10% mutational frequency. TCGA indicates The Cancer Genome Atlas.